CP2K

For pre-/post-processing of CP2K, you might also be interested in pycp2k and cp2kdata.

Generate input files: Cp2kInput

Create cp2k input files.

from toolbox.utils import *
from toolbox.io.cp2k import Cp2kInput

atoms = io.read("coord.xyz")
# remember to set cell parameters and pbc!
cp2k_inp = Cp2kInput(atoms=atoms, input_type="energy", cutoff=1000)
fp_params = {
    "FORCE_EVAL": {
        "DFT": {
            "SCF": {
                "MAX_SCF": 3,
                "EPS_DIIS": 1e-15,
                "DIAGONALIZATION": {"_": ".FALSE."},
                "MIXING": {"ALPHA": 0.0, "METHOD": "DIRECT_P_MIXING"},
            }
        }
    }
}
cp2k_inp.write(output_dir="test", fp_params=fp_params)

You can modify the internal template by setting the variables when initializing the Cp2kInput or via the dict fp_params.

Run CP2K calculation in python

You can perform CP2K calculations in python script via Cp2kCalculator.

Post-processing of output files

Cp2kOutput

Read data from cp2k standard output (for single frame). All output values have been converted to eV (from Hartree).

from toolbox.io.cp2k import Cp2kOutput

cp2k_out = Cp2kOutput("output.out")
print(cp2k_out.fermi)
print(cp2k_out.energy)

Cp2kCube and Cp2kHartreeCube

Read and do the average of cp2k cube file. In Cp2kCube, no unit conversion is taken. In Cp2kHartreeCube, atmoic unit of energy (i.e. Hartree) is converted to electron volt (eV).

from toolbox.utils import *
from toolbox.io.cp2k import Cp2kCube, Cp2kHartreeCube

e_cube = Cp2kCube("cp2k-TOTAL_DENSITY-1_0.cube")
output = e_cube.get_ave_cube(axis=2, gaussian_sigma=0.0)
plt.plot(output[0], output[1])

v_cube = Cp2kHartreeCube("cp2k-v_hartree-1_0.cube")
output = v_cube.get_ave_cube(axis=2, gaussian_sigma=0.0)
plt.plot(output[0], output[1])

plt.show()